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Morphological and Molecular Characterization of Proteus mirabilis Isolated from Different Clinical Samples in Najaf province

Assist .Lec.Khitam Abdul Kadhim mohsin Al-mashhadi(1) and Prof. DrBasaad Abedzaid Al- Fatlawi(2)

1.2.Faculty of Science ,Dep. of Biology / University of Kufa, Najaf,Iraq.

Email : [email protected]


The study included two main parts ,the first was the bacterial diagnosis based on relied diagnostic procedures .Second part were genetic study to virulence factors to common bacteria .A total of 148 samples were collected from different sources of patients that including (urine , vagina swab ,sputum ,tonsil) and from both sexes during a period from August 2020 to November 2020.

These patients ranged from 1-69 years.(85) of them were females and (48)were males .The result indicated ,the most age group were more susceptible to infected (20_29) year from other age group, represented 75 patients with a percentage of (56.3%), among this group females were more susceptible with percentage (63.9%) compared to males (36%).

The result indicated 133 samples (89.86%) gave positive result , while 15 samples (10.13%) was Negative for culture bacteria , primary identification was depended on biochemical tests .Finally identification with Vitek 2 system was done .The results demonstrate 42 isolate E.coli ,31 isolate P.mirabilis ,25 isolate K.pneumoniae , 21 isolate staphylococcus spp ,7 isolate streptococcus spp,3 isolate pseudomonas spp and 4 isolate other bacteria .All isolates (100%) of E.coli and K.pneumoniae were able to produce capsule and biofilm .

Regarding antibiotic susceptibility testing P. mirabilis isolates were resistant to Penicillin and sensitive to Amikacin .

The result indicated allP .mirabilis ,contain motA and motB genes contain motA which play role in the rotary motor of flagella with percentage 100%.

Key word:Morphological ,Proteus mirabilis,clinical samples and Najaf province.


P. mirabilis is one ofopportunistic pathogen, which can cause severe invasive diseases, Critically, in patients who are immunocompromised(1). This bacterium is one of main source of nosocomial


infections(2). P. mirabilis is also the one of causative agents of urinary tract, burns, respiratory, ear and otitis infections(3).

This bacteriumhas wide virulence factors that help to colonize, survive and grow in the host organism such as adhesion, swarming, fimbriae, urease and protease (4). Furthermore, it is well known that P. mirabilis can form biofilms. These biofilms colonize the airways, and provide a highly resistance of antibiotics (5). These abilities to from biofilm and have a resistance of antibiotics could acquire from different sources such as external environment, transferring gene from different species or strains( 6) .

The aim of this study

1.s specimens were collected from (urine ,vaginal swab, tonsillis and sputum,) for bacteriological study.

2.Identification of bacterial isolate by using cultural ,biochemical characters and vitek2 technique.

3.Determine P.mirabilis that isolated from (urine ,vaginal swab ,tonsillis and sputum).

4.Detection of some virulence factors of common isolated bacteria and Detection the existence of gene coding for some virulence factors using PCR technique .

Specimens Collection

A total of 148 specimens,133 (89.8 %) specimens revealed positive culture on blood agar and MacConky agar, while 15 (10%) specimens were no growth appear on MacConky agar and blood agar.,were collected from patient suffering from (urine ,sputum , tonsillitis and vaginal) infections during the proid From August 2020 to November 2020, and collected from patients suffering from different clinical specimens from AL-Sader Teaching Hospital , AL-Furat Alawsat Hospital,AL- sajad Hospital and private clinic in Al–Najaf province. Those specimens were collected from patients included both sex (male and female) and age range from 1 to 70 years. Swab was taken swab from infection area and then transport the swab by transport media to the lab.Data about type of infection, sex and age of patients were recorded on the swab. Specimens were collected from patients that not received antibiotic for one week before sample collection. All information, like date, sex, and age were recorded in questionnaire, sheet paper.

Specimens Culture

The collected specimens were inoculated on two types of culture media which included blood agar and MacConkey agar, and spread on the each plates with sterile loop. Plates were incubated at


37˚C for 24 hrs. The plates were examined there after for bacterial growth and plates were then a single pure isolated colony was transferred to Brain Heart Infusion agar for the preservation and to submitted the morphological evaluation by Gram staining and carry out other biochemical tests that confirmed the identification of isolates. After incubation period the isolates were identified according to (7).

Vitek – 2 for Identification

GN and GP identification card has been used for identification Gram positive and Gram negative bacteria . The bacterial suspension was adjusted to McFarland standard of 0.5 in 2.5ml of a 0.45% sodium chloride solution with a Vitek -2 instrument(bioMérieux, France). The time between preparation of the inoculum and the card filling was always less than 30 min. The GN identification card is a fully closed system to which no reagents have to be added. The card was put on the cassette designed for use with the Vitek–2 system, placed in the instrument, automatically filled in a vacuum chamber, sealed, incubated at 35.5˚C, and automatically subjected to colorimetric measurement (with a new reading head) every 15 min. for a maximum incubation period of 8 hours.

Data were analyzed, using Vitek –2 database, which allows organism identification in a kinetic mode beginning 180 min after the start of incubation (8)

Detection of Biofilm formation

Suspension of tested strain was incubated in the glass tubes containing Brain Heart infusion Broth (BHI broth)aerobically at the temperature of 35 ˚C for the period of 2days .Then the supernatant was discarded ,the glass tube has been stained by 0.1% safranin solution ,washed with D.W. three times and dried .In the case of biofilm formation ,a grainy red structure on the test tube bottom was found.(9)

Antibiotic Sensitivity Test

This test performed by Kirby-Bauer method as the following:

1- From new pure culture plate, 4-5 colonies of bacterial isolate were picked up by sterilized inoculating loop and emulsified in 5ml of sterile normal saline until the turbidity is approximately equivalent to that of the McFarland No. 0.5 turbidity standard which prepared as mentioned .


2- A sterile swab was dipped into bacterial suspension.

3- The surface of a Mueller-Hinton agar plate was streaked with the swab, then the plate was rotated through a 45º angle and streaked the whole surface again; finally the plate was rotated another90º and streaked once more. 4- By a sterile forceps the antimicrobial disc was picked up and placed on the surface of the inoculated plate, the disc was pressed gently into full contact with the agar.

5- The step (4) was repeated to all antimicrobial discs under the test, spaced evenly a way from each other.

6- The inoculated plates were incubated at 37ºC for 18-24 hours.

7- After incubation, the plates were examined for the presence of inhibition zone of bacterial growth (clear rings) around the antimicrobial discs, if there was no inhibition zone the organism was reported as resistant to the antimicrobial agent in that disc. If a zone of inhibition surrounded the disc, the diameter of the zone of inhibition was measured (by millimeters) and compared to standard results being recommended by clinical laboratory standards institute documentations (10) .

Extraction and Isolation of DNA

After culturing on MacConkey agar, isolates E.coli, Proteus mirabilis, and Klebsilla pneumonia, which are individually inoculated into broth and incubated at 37°C for 24 hours. The Genomic DNA Extraction Kit (Intron Korea) was used to extract DNA according to the manufacturer's instructions.

1- Transfer the appropriate amount of bacterial suspension to 1.5 ml micro centrifuge tube and centrifuge at full speed 13,000 rpm for 1 min, then discard the supernatant.

2- Add 200 μL of buffer CL, 20 μL proteinase K, and 5 μL RNase resuspend the pellet by vortex, incubate lysate at 56˚C using water bath for 20 min .

3- Add 200 μL of buffer BL into upper sample tube and mix thoroughly , then incubate the mixture at 70˚ C for 5 min .

4- Centrifuge the sample tube at 13,000 rpm for 5 min to remove un-lysed tissue particles , then


carefully transfer 400 μL of the supernatant into a new 1.5 ml tube.

5-Add 200 μL of absolute ethanol into the lysate.

6-Transfer the mixture to the spin column (in a 2 ml collection tube ) and centrifuge at 13,000rpm for 1 min . discard the flow through and place the spin column in a new 2 ml collection tube .

7- Washed the spin column with 700 μL of buffer WA and centrifuge for 1min at 13,000 rpm . discard the flow –through and reuse the collection tube, add 700 μL WB to the spin column and centrifuge for 1min at 13,000 rpm , discard the flow –through and place the column into a new l.5 ml collection tube.

8- To elution ; 100 μL of buffer CE was added directly onto the membrane . Incubate for 1 min at room temperature , then centrifuge for 1min at13,000 rpm to elute.

Estimation of DNA Concentration and purity

The extracted DNA was checked by using Nano drop spectrophotometer, which measured DNA concentration (ng/uL)and check the DNA purity by reading the absorbance at (260/280nm)as following seps:

1.after opening up Nanodrop software,chosen the appropriate application (Nucleic Acid ,DNA).

2.A dry wipe was taken to clean instrument pedestals several time .then carefully pipette 2ul of add H2O on to the surface of the lower measurement pedestals for blank system

3.The sampling arm was lowered and clicked OK to initialized the Nano drop ,then cleaning off the pedestals and 1ul of extracted DNA carefully pipette onto the surface of the lowered measurement pedestals, then concentration and purity of extracted DNA was checked ( 11).

Polymerase Chain Reaction (PCR) Assay

PCR assay was performed in monoplex pattern in order to amplify different fragments of genes under study for detecting of K.pneumoniae E.coli and P.mirabilis virulence factors of 6 genes from each type were selected to be amplified separately in monoplex PCR technique used in this study table (1)


Table (1): Determining virulence genes and encoding propertie

Table (2) Primers (Macrogen, Europe) used in the study Type



Type Primer Sequence (5'-3') amplicon

size(bp) Reference

P. mirabilis





Table (3): PCR program that apply in the thermo-cycler

Cycle s Num ber Temperature(°C)

/Time Gene

type of

bacteria Final

Extensio n Condition of one cycle

Initial Denaturati

on Extensio

Annealing n Denaturati


30 72\5min.


52\ 30 sec.

94 \ 30 sec.

94\ 3 min.

motA Proteus


30 72\5min

72\1 min 52\30 sec.

94 \30 sec.

94\3 min.


Agarose Gel Preparation and DNA Loading This procedure was used in accordance as follows:

1. 2g of agarose was dissolved in 100 ml of Tris-borate-EDTA (TBE) (90 ml distilled water + 10 ml TBE) with final concentration 10x

2. The Tris-borate-EDTA solution was boiled, then cooled to 45°C before adding 0.5 mg/ml ethidium bromide..

3.The agarose poured in equilibrated gel tray, and left until cooled and became more hardened.

3. Five microliters of PCR product were loaded to each of agarose gel wells inaddition to one for Encoding protein

Genes type bacteria

swarming motility motA

P. mirabilis

Outer membrane lipoprotein MotB


DNA marker , the gel tray was fixed in electrophoresis chamber and TBE buffer was added to thechamber. The electric current wasperformed at 70 volt for 80 Minutes.

4. Finally, the electrophoresis result was detect using gel documentation system,the positive

results were proved when the DNA band base pairs of sample equal to the target product size .

Results and Discussion Isolation and Identification

During the study period from August 2020 to November 2020,the total of 148 clinical specimens were collected from patients sufferingfrom different infections( urine,vagnial swab,tonsillis and sputum). The results showed that 133 (89.8 %) specimens revealed positive culture on differential media , while 15 (10%) specimens were no growth.infections to each gender : female 85(63.9%) specimens and male 48(36%) specimens.This study agree with (14) they found that E.coli prevalence in female was 68% and male 32%.The result of this study agree with (15)was more in female patients compared with male patients probably because the number of patients admitted was more than male patients ,the sexual dimorphism in bacterial infections has been mainly attributed to the differential levels.of sex hormones between males and females as well as to genetic factors.(16)(17),with age group from 1-69 years old.In the current study, the prevalence types of infections based on patients age and gender in different groups were shown in table (4).

The highest appeared at the20-29age group that 75(56%) ,these results agree with(18)which was percentage in adult.The cause for such high percentage in young may be due to cross infection because of overcrowded class rooms ,work place ,ventil action in this places and more transfer persens in this age ( 19) .The lowest incidence was among the (50-59) age . The patient's age ranged from (1-69) years old. The age distribution of the patients can be seen in table (4).

Table (4): Distribution of bacterial isolate according to age and gende

Age NO male female

1_10 7(6.7%) 5(10.4%) 2(2.3%)

10_19 8(7.5%) 1(2%) 7(8.2%)

20_29 75(56.3%) 25(52%) 50(58.8%)

30_39 23(17.2%) 10(20%) 13(15.2%)


Biochemical tests of bacterial species that causes of infections :

Many bacterial isolates were diagnosed by using the bacterial cultured, Gram stain ,morphology and biochemical tests ,for the bacterial were isolates and investigated in the laboratory . (7)

Table (5) : Biochemical test of bacterial species that causes of infections:

test bacterial

catalase coagulase oxidase indole methyl red


proskauer urease motility E.coli + _ _ + + _ _ +

p.mirabilis + _ _ + + _ + +

k.pneumonia + _ _ _ _ + + _

staphylococcus ssp + + _ _ + + + _

streptococcus spp _ _ _ _ + _ _ _

pseudomonas spp + _ + _ _ _ _ v

The final identification was performed with the automated VITEK-2 compact system using GP,GN- ID cards which contained 64 biochemical tests and one negative control. Exactly 133 isolates performed identification and confirmed by Vitek-2 system by using Kit(GP-ID cards) to Gram positive bacteria and Kit(GN-ID cards) to Gram negative bacteria.These Isolates grown on blood agar,manitol agar and MacConky agar,and appear positive and negative to Gram stain ,they have been elected bacterial species E.coli , P. mirabilis,K. pneumonia , Staphylococcu spp (aureus,epidermis and maraxella), streptococcus spp(pneumonia,pyogen and agalactie) , pseudomonas spp (aeraginosa and fluorescence) and enterobacteraerogenes, burkholderiapseudomallei sphingomonas paucimobilis , which the most frequently than the rest bacteria that neglected recurrence rates,the most common pathogen was E.coli 42 (31.5%)The morphological characterization of bacteria in table (6) rareled that the P.mirabilis were 31(23.3%) which appeared small in size, Gram negative bacteria and gave negative result for (oxidase ,vp and Hemolysin)while positive result for (catalase, indole and urease).This study similar to study for(20)they found P.mirabilis 40(19.5%) isolated from different source. Many studies were reported that P.mirabilis was the important agent causing different types of infection, in particular or

40_49 10(7.5%) 3(6.2%) 7(8.2%)

50_59 2(1.5) _ 2(2.3%)

60_69 8(6%) 4(8.3%) 4(4.7%)

total 133(100%) 48(36%) 85(63.9%)


UTI,(21)recorded in their study that P.mirabilis was accounted (54%)of bacterial isolates (22) found that (77%)of isolates were identified P.mirabilis and the bacteria in the study of (23)were recorded in (65%) of isolates .In contrast, (24)demonstrated that(15%) of isolates were P.mirabilis and (25)found (3%) of urine isolates were P.mirabilis .(26)found 45(75%) from different result source infection .These different may be due to differentiation in the source of infection ,condition of the collection and identification methods. Twenty five isolates (18.7%) of K.pneumoniae.

Table (6) : The positive results of bacterial isolates

type of bacteria No. of bacteria percent

E.coli 42 31.5%

p. mirabilis 31 23.3%

k. pneumonia 25 18.7%

staphylococcus spp 21 15.7%

streptococcus spp 7 5.2%

pseudomonas spp 3 2.2%

other bacteria 4 3%

total 133 100%

Fig (1): The positive results of bacteria isolates

Disturibution of E.coli , P.mirabilis and K. pneumonia isolates according to the source.

Most of isolate78 (58%) isolates were recovered from urine specimens ,29 (21.8%) isolates

E.coli, 42

P.mirabilis, 31 K.pneumona, 25

Staphylococcus spp, 21 Streptococcus

spp, 7

Pseudomonas spp, 3

other bacteria , 4


from vaginalswabs ,16( 12% ) isolates from tonsillist and10 (7.5%) isolates from sputum.table (7) In this study was many isolation bacterial from different sample , the important agent causing different types of infection, in particular UTI ,Genital tract infection,tonsillist and respiratory urine specimens the high presented bacterial E.coli 36 (46%), P.mirabilis 15(16%)and K.pneumonia 7 (8.9%) while vaginal swab the high commonly bacterial K. pneumonia 12(41.3%) , P.mirabilis11(37.5%) and E.coli 3(10%). Tonsillist P. mirabilis 3(18.7%), E.coli 2(18.5%)and k.pneumonia1(6.2%), sputum K.pneumonia 5(50%) P.mirabilis 2(20%) and E.coli 1( 10%).These results were agreed with many previous studies such as that established by(27)(14 ),who found that E.coli was the commonest member of Entero bacteriacea that can cause severe infections.many studies were reported that p.mirabilis was the important agent causing different types of infection,


who formed that p.mirabilis was couse many infection .This study agree with(30)(31) who found that K.pneumoniae was the commonest member of Klebsiellaspp.that can cause severe infections.Among all patients diagnosed with K.pneumonia.(32).

Table(7) Disturibution of E.coli ,p.mirabilis and k. pneumonia isolates according to the source.

type of

specimens NO E.coli

proteus mirabilis

Kebsiella pneumonia

Staphylococcus spp

Streptococcus spp

other bacteria

urine 78(58%) 36(46%) 15(19%) 7(8.9%) 15(19.2%) 3(3.8%) 2(2.5%) vaginal


29(21.8%) 3(10%) 11(37.9%) 12(41.3%) 0 1(3.4%) 2(6.8%)

tonsillist 16(12%) 2(12.5%) 3(18.7%) 1(6.2%) 5(31.2%) 3(18.7%) 2(12.5%)

sputum 10(7.5%) 1(10%) 2(20%) 5(50%) 1(10%) 0 1(10%)

total 133(100%) 42(31.5%) 31(23%) 25(18.7%) 21(15.7%) 7(5.2%) 7(5.2%)


Fig(2):Disturibution of type bacteria isolates according to the source.

Detection of some virulence factors for bacteria caspsule production

The results revealed that capsular phenotype was investigated among E.coli and K.pnemoniae isolates ,the results showed that all E.coli and K.pneumoniae isolates (100%) were positive for capsule production .These results in the present study agreed with(14)(33)They found that capsule production is considered as an important virulence factors in bacterial pathogenicity because capsular material forms thick bundles of fibrillous structures covering the bacterial surface in massive layers.

Anew hypervirulent ( hyper mucoviscous) variant of some bacteria has emerged.Defining clinical features are the ability to cause serious ,Life threatening community-acquired infection in younger healthy hosts, including liver abscess, pneumonia, meningitis and endophthalmitis and the ability to metastatistically spread ,an unusual feature for enteric Gram-negative bacilli in the non- immunocompromised (34) The polysaccharide capsule is amony the most important virulence determinants, providing protection from phagocytosis,resistain to complement-mediated killing and suppression of human beta-defensin expression(15).

Biofilm production

The results of this study showed that most isolates of bacteria had ability to biofilm formation, This result were agreed with the result study of (20) .they showed that 60% of P.mirabilis strain were biofilm producers and agree with(36) (37)( 38)

. In nature bacteria can exist in planktonic and biofilm embedded state( 39) .Biofilm growth is the most predominant made of growth for bacteria within the environment and is likely a survival mechanism.


3 2 1



3 2




5 15



3 1 3 1

2 2 2 0 1

urine vaginal swab tonsillist sputum

E.coli P.mirabilis K.pneumonia

staphylococcus spp streptococcus spp other bacteria


A biofilm is a bacterial population that is adherent to biological or non-biological surface and is enclosed by an extra-polymeric substance .Biofilm development is a sequential process initiated by the attachment of planktonic cells to a surface ,which is followed by formation of micro colonies and biofilm maturation in which individual bacteria , as well as the entire community are embedded in a matrix composed of nucleic acid, protein and polysaccharides (40) .Microorganisms form biofilm , that exist in the environment .whether upon inanimate objects or living animals, the bacteria attach to these surfaces, including soli and aquatic systems, and have been documented in the human literature developing on medical devices ,within the middle ear, external ear ,lunges, heart valves ,surgical implants and tooth enamel (41).

Biofilm formation in Gram negative bacteria occurs when bacteria cells first swing along a surface ,using Flagellar-mediated motility, until attachment occurs at a specific site and their attachment is initially reversible (42).Initial growth of bacteria is the production of Microcolonies(clusters of cells),which form when cells aggregate together. With further movement of the cells using type IV pili-known as twitching motility, the attachment becomes irreversible.

This will develop once surface interactions are stable.(43). Antimicrobial Susceptibility Test

Many factors have contributed to high antibiotics resistance rates in Iraqi hospitals and community , such as excessive antibiotics prescription, antibiotics can be purchased without a prescription and inadequate surveillance also account for the spread of resistance bacteria , The results revealed that showed different degrees of resistance to antibiotics that used in the study. P. meribilisthe results showed that most of the bacterial isolates were resistance Penicillins 31 (100%) this result agree with(44)Similar results were found in the results of( 45). However, the study reveals that P.mirabilis was high sensitive to Imipenem (100%), such results were found in a study of( 46)(47)( 48)

were documented that the sensitivity of P.mirabilis is 100% to this antimicrobial. but were different from the results of( 48)(49). Some P. mirabilis isolates present an elevation in the resistance level to Imipenem due to many reasons: the loss of outer membrane porins, decreased expression of PBP1a or reduced binding of Imipenem by PBP2 (50). (51)

noted that the development of resistant against imipenem in Proteus mirabilis is due to the absence of 24 kDa OMP.

Amikacin is an amino-glycoside antibiotic used to treat different types of bacterial infection. It is works by binding to the bacterial 30s ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. In this study P.mirabilis isolate show


high sensitivity to Amikacin (100%), These result confirmed with result by(52) ( 47) (48) (53)

found the percentage of susceptibility to Amikacin was 87% to98%, which considered an agreement to this result.and other results dis agree with (28).

Tobramycin result showed (100%) of the isolates of P.mirabilis were sensitive to this antimicrobial, A study by(54) found the percentage of resistance was (40%) Tobramycin and( 55) which considered an disagreement to this result, reported that the Tobramycin was not able to inhibit the growth of proteus species more than 34%.

Table (8):Determination the sensitivity of the bacteria to antibiotics

no type of antibiotics



1. Penicillins (p) 0 31(100%)

2. Amoxicillin/clavulanic acid(AMC)

6(19.3%) 25(80%)

3. Imipenem(IMP) 31(100%) 0

4. Cefotaxime (CTX) 28(90%) 3(9.6%) 5. Ceftriaxone (CRO) 21(67%) 10(32%) 6. Ceftazidime (CAZ) 27(87%) 4(12.9%) 7. Gentamicin (CN) 25(80.6) 6(19.3%)

8. Amikacin (AK) 31(100%) 0

9. Tobramycin (TOB) 31(100%) 0

Molecular Detection of P.mirabilis Isolates

The verulence genes motA and motB carried on P.mirabilis DNA were investigated these genes have a major role to induce many of p.mirabilis infections(12)(13).The polymerase chain reaction was used to detect the predominant of those genes in bacterial isolates using specific primer for each one ,the results appear that all isolates (100%) were carrying motA and motB fig(3) and fig (4).The matA and motB genes play a role in the rotary motor of flagella(56) .The two motA and motB genes are required for swimming and twitching motility of p.mirabilis the stator complexes are not only in p.mirabilis but also in most pathogenic bacteria that need to swarm in over surfaces .(57).These results were similar with the result of, ( 20) (58) (4)

who reported that the genes were encoded in


chromosomal DNA of p.mirabilis strain.

Figure (3): Ethidium bromide-stained agarose gel electrophoresis of PCR products from extracted total DNA of P.mirabilis using primer motA gene with product (215bp). The electrophoresis was performed at 70 volt for 1.5-3hr. lane (L), DNA molecular size marker (100 bp ladder). Lanes (1 to5) show positive results with gene mot A.

Figure (4): Ethidium bromide-stained agarose gel electrophoresis of PCR products from extracted total DNA of P.mirabilis using primer motB gene with product 150bp. The


electrophoresis was performed at 70 volt for 1.5-3hr. lane (L), DNA molecular size marker (100 bp ladder). Lanes (1 to5) show positive results with gene motB.


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